I mostly use ems for vertical margins on elements like p elements and headings but would not use them for for horizontal margins because the margin would be different depending on the font size of the element so they would never align in a straight line. The benefit of ems for vertical margins is that the bigger the text then the bigger the gap is proportionately.

When using ems for containers like divs you must ensure they are all the same font-size to start with then otherwise horizontal em margins would be of no use as they would not line up either.